The difference is that EEG can be used usefully in e.g. biofeedback training and the study of sleep phases, so there is in fact enough signal here for it to be broadly useful in some simple cases. It is not clear fMRI has enough signal for anything even as simple as these things though.
I have been told QEEG can offer an additional perspective in neurofeedback, etc as well.
fMRI's are being used in TBI/Concussion recovery that are study backed and seem to be delivering results.